6p21.2CNV Type: Deletion-Duplication
Largest CNV size: 45218 bp
Statistics Box:
Number of Reports: 10
Number of Reports: 10
Summary Information
Summary statement in development
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
Identifying autism loci and genes by tracing recent shared ancestry.
Deletion
Identification of candidate intergenic risk loci in autism spectrum disorder.
Deletion-Duplication
Convergence of genes and cellular pathways dysregulated in autism spectrum disorders.
Duplication
Excess of rare, inherited truncating mutations in autism.
Deletion-Duplication
Minor Reports
Title
Author, Year
Report Class
CNV Type
Reduced transcript expression of genes affected by inherited and de novo CNVs in autism.
Deletion
Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.
Deletion-Duplication
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Deletion-Duplication
Performance of case-control rare copy number variation annotation in classification of autism.
Duplication
Chromosomal microarray analysis in clinical evaluation of neurodevelopmental disorders-reporting a novel deletion of SETDB1 and illustration of cou...
Duplication
Paternally inherited cis-regulatory structural variants are associated with autism.
Deletion
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
brandler_18_ASD_replication_cases
Affected individuals from MSSNG cohort (1395 cases from 1187 families) and the Simons Simplex 2 (SSC2) cohort (584 cases from simplex quad families)
1979
Cases diagnosed with ASD
N/A
N/A
3025
1
0
1
engchuan_15_ASD_discovery_cases
Samples from the Autism Genome Project (AGP)
1892
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
N/A
85.78% Male
86425
0
2
2
krumm_15_ASD_discovery_cases
Probands from the Simons Simplex Collection
2377
Diagnosis of ASD
N/A
N/A
140511
2
1
3
morrow_08_ASD_discovery_cases
Affected individuals from 70 families (52 simplex, 18 multiplex) recruited by Homozygosity Mapping Collaborative for Autism (HMCA) used in CNV analysis. This cohort was selected from an original population of affected individuals from 104 families (79 simplex, 25 multiplex; 82.7% male); 88 of these pedigrees have cousin marriages.
94
ASD (based on DSM-IV-TR diagnoses when research scales not available in native language)
18651
2
0
2
nord_11_ASD_discovery_cases
Youth with ASD (as part of mother-father-child trios)
41
ASD
85.4% Male
36515
1
0
1
pinto_14_ASD_discovery_cases
ASD probands from simplex and multiplex families collected as part of stage 2 of the Autism Genome Project (AGP) after quality control (1,604 before QC)
1359
Cases classified according to ADOS and ADI-R
N/A
N/A
86426
0
1
1
prasad_12_ASD_discovery_cases
Unrelated ASD cases recruited from three Canadian sites (Hospital for Sick Children, McMaster University, and Memorial University of Newfoundland); the majority of cases had been previously genotyped with results published in Marshall et al., 2008 and Pinto et al., 2010. 20 cases from initial cohort of 696 were excluded from further analysis (due to CNVs > 5 Mb).
676
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS
NA
82.84% Male
194483
2
4
6
sanders_11_ASD_discovery_cases
Autistic probands from the Simons Simplex Collection (SSC). 872 probands in quartet families, 272 probands in trios.
1124
ASD diagnosis: 89.5% autism; 8.5% PDD-NOS, 2% Asperger syndrome. Mean full-scale IQ 85.1 1.5 (mean verbal IQ, 81.9 1.7; mean non-verbal IQ, 88.4 1.4)
Mean, 9.1 yrs.
86.1% Male
45218
6
1
7
walker_13_ASD_discovery_cases
Unrelated ASD probands previously described in Lionel et al., 2011 and Pinto et al., 2010 CNV reports
1491
Diagnosis of ASD based on gold-standard instruments including ADI and ADOS.
N/A
N/A
56618
2
2
4
xu_16_ASD/DD/ID_discovery_cases
Patients referred to the Duke Autism Genetics Clinic for clinical genetic evaluation of ASD and DD/ID from 2010-2014
115
66 cases with confirmed primary diagnosis of ASD (DSM-IV, DSM-5, ADOS, and ADI-R used to support ASD diagnosis), 49 cases with primary diagnosis of DD or ID (based on IQ and DQ scores).
Range, 18 months-15.1 years (mean age, 5.7 years)
72.17% Male
1000000
0
1
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
engchuan_15_ASD_discovery_controls
Platform-matched controls from three large studies: SAGE (Study of Addiction Genetics and Environment), Ontario Colorectal Cancer study, and HABC (Health Aging and Body Composition)
2342
Controls; subjects had no previous psychiatric history
N/A
46.67% Male
261383
0
2
2
krumm_15_ASD_discovery_controls
Unaffected siblings from quad families from the Simons Simplex Collection
1786
Control
N/A
N/A
0
0
0
0
levy_11_ASD_discovery_controls
Unaffected siblings of autistic probands from 887 families from the Simons Simplex Collection (SSC)
863
Control
47.97% Male
116776
1
0
1
nord_11_ASD_discovery_controls
Samples from 367 total control individuals (319 European American, 48 African American) used to test for differences in rare CNV prevalence compared with autism cases
123
Controls (no history of psychiatric symptoms by self-report)
30 yrs.
0
0
0
0
prasad_12_ASD_discovery_controls
PDx controls [1000 DNA samples from reportedly healthy donors (50.2% male) from BioServe (Beltsville, MD)] and 4139 in-house controls previously reported in Krawcak et al. 2006, Stewart et al. 2009, and Bierut et al. 2010. CNVs identified in controls were used to define rare ASD-specific CNVs.
5139
Control
NA
NA (PDx controls 50.2% male)
194483
0
0
0
sanders_11_ASD_discovery_controls
Matched siblings of autistic probands from the Simons Simplex Collection (SSC).
872
Controls
Mean, 10.0 yrs.
18482
3
1
4
walker_13_ASD_discovery_controls
Control samples from the SAGE cohort (n=1287), from the Ottawa Heart Institute (n=1234), and from the POPGEN collection (n=1123)
3644
Control
N/A
N/A
56618
0
0
0
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
brandler_18_ASD_replication_cases
N/A
WGS
Illumina HiSeq X10
ForestSV, Lumpy, Manta, Mobster, SV2
None
engchuan_15_ASD_discovery_cases
Caucasian
Solid phase hybridization
Illumina 1M
None
krumm_15_ASD_discovery_cases
N/A
WES
CoNIFER, XHMM
Solid phase hybridization (Illumina 1M, 1 M Duo, or Omni 2.5)
morrow_08_ASD_discovery_cases
Arabic Middle East, Turkey, and Pakistan
Array SNP
Affymetrix 500K
BRLMM
dChip
PCR
nord_11_ASD_discovery_cases
29 European American, 3 Asian American, 2 Hispanic, 2 African American, 5 unknown ancestry
aCGH
NimbleGen HD2
Sliding-window algorithm, ~10 kb minumum size threshold
None
pinto_14_ASD_discovery_cases
Predominantly European
Solid phase hybridization
Illumina 1M (v.1 and v.3)
qPCR, MLPA, long-range PCR
prasad_12_ASD_discovery_cases
Canada
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
None
sanders_11_ASD_discovery_cases
White non-Hispanic, 74.5%; mixed, 9.3%, Asian, 4.3%, White Hispanic, 4.0%, African-American, 3.8%; other, 4.2&
Solid phase hybridization
Illumina 1M v1, Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
walker_13_ASD_discovery_cases
N/A
Array SNP, solid phase hybridization
Illumina 1M, Affymetrix 6.0
QuantiSNP, PennCNV, Birdsuite, iPattern, Affymetrix Genotyping Console
Long-range PCR, qPCR
xu_16_ASD/DD/ID_discovery_cases
N/A
aCGH, array SNP
BlueGnome CytoChip v2, Affymetrix 6.0, Affymetrix Cytoscan HD
Affymeytrix Genotyping Console v3.0.2
None
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
engchuan_15_ASD_discovery_controls
Caucasian
Solid phase hybridization
Illumina 1M
None
krumm_15_ASD_discovery_controls
N/A
WES
CoNIFER, XHMM
None
levy_11_ASD_discovery_controls
aCGH
NimbleGen HD2
HMM
nord_11_ASD_discovery_controls
aCGH
NimbleGen HD2
Sliding-window algorithm, ~10 kb minumum size threshold
None
prasad_12_ASD_discovery_controls
NA
aCGH
Agilent 1M
ADM-2, DNAcopy (R Bioconductor)
DNA Analytics v4.0.85 (Agilent), DNAcopy
sanders_11_ASD_discovery_controls
Solid phase hybridization
Illumina 1M v1 or Illumina 1M v3
PennCNV, QuantiSNP, GNOSIS
walker_13_ASD_discovery_controls
N/A
Array SNP, solid phase hybridization
Illumina 1M, Affymetrix 6.0
QuantiSNP, PennCNV, Birdsuite, iPattern, Affymetrix Genotyping Console
None
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
brandler_18_ASD_replication_cases-caseSSC11070
N/A
M
ASD
Case from SSC_phase2 cohort
37690685
37693709
3025
GRCh38
Deletion
No
engchuan_15_ASD_discovery_cases-case20054_1280001
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
38153435
38239860
86426
GRCh38
Duplication
No
engchuan_15_ASD_discovery_cases-case5083_3
N/A
N/A
ASD
Diagnosis of ASD based on Autism Diagnostic Observation Schedule (ADOS) and Autism Diagnostic Interview-Revised (ADI-R)
39947610
39986438
38829
GRCh38
Duplication
No
krumm_15_ASD_discovery_cases-case11051.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
38592575
38598094
5520
GRCh38
Deletion
Yes
krumm_15_ASD_discovery_cases-case12211.p1
N/A
Female
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Quad
158789287
158818093
28807
GRCh38
Duplication
Yes
krumm_15_ASD_discovery_cases-case12212.p1
N/A
Male
ASD
Proband from the Simons Simplex Collection (SSC). Family type: Trio
107193821
107334332
140512
GRCh38
Deletion
Yes
morrow_08_ASD_discovery_cases-case5101
NA
ASD
NA
NA
37410410
37441296
18651
Unknown
Homozygous deletion
Yes
nord_11_ASD_discovery_cases-239-1
ASD
40174690
40211204
36515
Unknown
Deletion
No
pinto_14_ASD_discovery_cases2-case20054_1280001
N/A
M
ASD
Clinical profile: N/A.
Cognitive profile: N/A.
38153435
38239860
86426
GRCh38
Duplication
Yes
prasad_12_ASD_discovery_cases-case102350
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
38952477
39146959
194483
Unknown
Duplication
No
prasad_12_ASD_discovery_cases-case146446L
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
39461456
39475490
14035
Unknown
Duplication
No
prasad_12_ASD_discovery_cases-case160012L
NA
F
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
40174704
40203990
29287
Unknown
Deletion
No
prasad_12_ASD_discovery_cases-case60416
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
38069512
38093797
24286
Unknown
Duplication
No
prasad_12_ASD_discovery_cases-case68672
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. Novel CNV
38069512
38093797
24286
Unknown
Duplication
No
prasad_12_ASD_discovery_cases-case99006
NA
M
ASD
Diagnosis of ASD based on meeting criteria on ADI-R and/or ADOS. CNV identified by previous SNP microarray study
40174704
40203990
29287
Unknown
Deletion
No
sanders_11_ASD_discovery_cases-11029.p1
9.3
F
Autism
NA
Full-scale IQ, 29; non-verbal IQ, 36; verbal IQ, 21
37549709
37594927
45219
GRCh38
Duplication
No
sanders_11_ASD_discovery_cases-11037.p1
9.3
M
Autism
NA
Full-scale IQ, 83; non-verbal IQ, 86; verbal IQ, 83
39101492
39104905
3414
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11051.p1
12.2
M
Autism
NA
Full-scale IQ, 106; non-verbal IQ, 102; verbal IQ, 114
38592439
38631790
39352
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-11677.p1
7.9
M
Autism
NA
Full-scale IQ, 101; non-verbal IQ, 100; verbal IQ, 103
37202646
37210007
7362
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12046.p1
12.6
M
Autism
NA
Full-scale IQ, 87; non-verbal IQ, 88; verbal IQ, 87
38012180
38047923
35744
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12224.p1
4.3
M
Autism
NA
Full-scale IQ, 80; non-verbal IQ, 85; verbal IQ, 78
40278083
40290441
12359
GRCh38
Deletion
No
sanders_11_ASD_discovery_cases-12429.p1
4.8
M
Autism
NA
Full-scale IQ, 74; non-verbal IQ, 71; verbal IQ, 82
37069894
37076277
6384
GRCh38
Deletion
No
walker_13_ASD_discovery_cases-case1-0381-003
N/A
M
ASD
N/A
N/A
40098471
40133607
35137
GRCh38
Deletion
Yes
walker_13_ASD_discovery_cases-case2-0139-003
N/A
M
ASD
N/A
N/A
39947610
39986438
38829
GRCh38
Duplication
Yes
walker_13_ASD_discovery_cases-case2-1368-003
N/A
F
ASD
N/A
N/A
40098471
40134977
36507
GRCh38
Deletion
Yes
walker_13_ASD_discovery_cases-case3-0139-000
N/A
M
ASD
N/A
N/A
39946181
40002798
56618
GRCh38
Duplication
Yes
xu_16_ASD/DD/ID_discovery_cases-case25
N/A
N/A
Developmental delay
Primary diagnosis of developmental delay based on DQ scores. Note: CNV coordinates in this report given as RP3-350J21->RP1-278E11 (chr6:39,977,164-40,076,642,gh17)
N/A
N/A
1000000
NCBI35
Duplication
No
Controls
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
engchuan_15_ASD_discovery_controls-controlHABC_902578_902578
N/A
N/A
Control
No previous psychiatric history
38163666
38233669
70004
GRCh38
Duplication
No
engchuan_15_ASD_discovery_controls-controlHABC_902652_902652
N/A
N/A
Control
No previous psychiatric history
36864327
37125710
261384
GRCh38
Duplication
No
levy_11_ASD_discovery_controls-11705.s1
NA
F
Control
NA
NA
40372548
40489323
116776
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11037.s1
6.5
F
Control (matched sibling)
NA
NA
39101492
39104905
3414
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-11563.s1
9.3
F
Control (matched sibling)
NA
NA
37901658
37911780
10123
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12434.s1
8.8
F
Control (matched sibling)
NA
NA
40279383
40290441
11059
GRCh38
Deletion
No
sanders_11_ASD_discovery_controls-12592.s1
10.1
F
Control (matched sibling)
NA
NA
38000231
38018713
18483
GRCh38
Duplication
No
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
brandler_18_ASD_replication_cases-caseSSC11070
No validation step reported
Paternal
MDGA1
engchuan_15_ASD_discovery_cases-case20054_1280001
Unknown
ZFAND3,BTBD9
engchuan_15_ASD_discovery_cases-case5083_3
Unknown
TUBBP9
krumm_15_ASD_discovery_cases-case11051.p1
Illumina 1M
Paternal
Simplex
Segregated
BTBD9
krumm_15_ASD_discovery_cases-case12211.p1
Illumina 1MDuo
Paternal
Simplex
Segregated
EZR-AS1,EZR
krumm_15_ASD_discovery_cases-case12212.p1
Illumina 1MDuo
Paternal
Simplex
Segregated
RPS24P12,PDSS2
morrow_08_ASD_discovery_cases-case5101
PCR
Both parents
NA
NA
Nearest to noncoding 5' RNF8
nord_11_ASD_discovery_cases-239-1
Paternal
0 genes
pinto_14_ASD_discovery_cases2-case20054_1280001
qPCR
Maternal
Simplex
(not tested)
ZFAND3,BTBD9
prasad_12_ASD_discovery_cases-case102350
Unknown
Unknown
Unknown
DNAH8,GLP1R
prasad_12_ASD_discovery_cases-case146446L
Unknown
Unknown
Unknown
KIF6
prasad_12_ASD_discovery_cases-case160012L
Unknown
Unknown
Unknown
0 genes
prasad_12_ASD_discovery_cases-case60416
Unknown
Unknown
Unknown
ZFAND3
prasad_12_ASD_discovery_cases-case68672
Unknown
Unknown
Unknown
ZFAND3
prasad_12_ASD_discovery_cases-case99006
Unknown
Unknown
Unknown
0 genes
sanders_11_ASD_discovery_cases-11029.p1
Maternal
Simplex (quad-proband matched)
Segregated
MIR4462
sanders_11_ASD_discovery_cases-11037.p1
Paternal
Simplex (quad-proband matched)
Not segregated
SAYSD1
sanders_11_ASD_discovery_cases-11051.p1
Paternal
Simplex (quad-proband matched)
Not segregated
BTBD9
sanders_11_ASD_discovery_cases-11677.p1
Paternal
Simplex (quad-proband matched)
Not segregated
sanders_11_ASD_discovery_cases-12046.p1
Both parents
Simplex (trio)
NA
ZFAND3
sanders_11_ASD_discovery_cases-12224.p1
Unknown
Simplex (quad-proband matched)
Segregated
sanders_11_ASD_discovery_cases-12429.p1
Paternal
Simplex (trio)
NA
walker_13_ASD_discovery_cases-case1-0381-003
Long-range PCR or qPCR
Paternal
Simplex
Segregated
walker_13_ASD_discovery_cases-case2-0139-003
Long-range PCR or qPCR
Maternal
Multiplex
Not segregated (duplication absent in affected sibling)
TUBBP9
walker_13_ASD_discovery_cases-case2-1368-003
Long-range PCR or qPCR
Maternal
Simplex
Segregated
walker_13_ASD_discovery_cases-case3-0139-000
Long-range PCR or qPCR
Unknown (not maternal)
Simplex
Unknown
TUBBP9
xu_16_ASD/DD/ID_discovery_cases-case25
Maternal
CNV gene content N/A (CNV start and end points N/A)
Controls
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
engchuan_15_ASD_discovery_controls-controlHABC_902578_902578
Unknown
BTBD9
engchuan_15_ASD_discovery_controls-controlHABC_902652_902652
Unknown
COX6A1P2,RPL12P2,PPIL1,C6orf89,MTCH1,FGD2,PI16
levy_11_ASD_discovery_controls-11705.s1
Paternal
Simplex
NA
RNU6-250P,TDRG1,LRFN2
sanders_11_ASD_discovery_controls-11037.s1
Paternal
Simplex (quad)
NA
SAYSD1
sanders_11_ASD_discovery_controls-11563.s1
Paternal
Simplex (quad)
NA
ZFAND3
sanders_11_ASD_discovery_controls-12434.s1
Unknown
Simplex (quad)
NA
sanders_11_ASD_discovery_controls-12592.s1
Maternal
Simplex (quad)
NA
ZFAND3
No Animal Model Data Available